How to convert VCF into hapmatrix format?
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2.1 years ago

Dear everybody,

I have a vcf file and I am using sfsR function of popseq package on R software. The link to package is http://rdrr.io/github/sdwfrost/popseq/man/sfsR.html#heading-5

It requires hapmatrix as input and I have no idea of hapmatrix file structure. Can anyone please help me how to convert my vcf into hapmatrix? By using which tool and what is its command? Any help would be highly appreciated.

Thanks in advance

popseq hapmatrix vcf • 729 views
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How did you pick this package? Are you following a workflow outlines somewhere?

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I found this package on github http://github.com/sdwfrost/popseq and then I installed this package on R. No, I am not following any outline as such.

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Installing random packages is not something you should be doing at this level - it is a more advanced challenge for once you're familiar with how to substitute parts of existing pipelines with your own plug and play modules.

Never a bad time to get started though, so congrats. Try to understand the haplotype matrix format and look for tools that can get you from VCF (or maybe a different upstream format) to that format. It might be a simple awk command once you understand the hapmatrix format well. Look at the information content in both formats and see if they're compatible.

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Thank you so much for your help.

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